Question

samtools -n flag

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4.7 years ago

wrab425 ▴ 50

I have a command

samtools bam2fq -n ......

can somebody tell me what the -n flag does?

Thanks

ChIP-Seq • 638 views

ADD COMMENT • link updated 4.7 years ago by ATpoint 86k • written 4.7 years ago by wrab425 ▴ 50

score 0 · Answer 1 · 2020-04-27

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4.7 years ago

ATpoint 86k

From the manual:

-n                   don't append /1 and /2 to the read name

It is okay to use that, some aligners like read names being identical for both mates.

ADD COMMENT • link 4.7 years ago by ATpoint 86k

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thanks once again ATpoint

ADD REPLY • link 4.7 years ago by wrab425 ▴ 50

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Sure thing.

ADD REPLY • link 4.7 years ago by ATpoint 86k